The red scar on the back of Cyclops' neck to signify his being controlled by Stryker was added digitally afterwards.

Originally the idea was that Jean Grey was temporarily rendered blind after her violent reunion with Cyclops. This was initially filmed as such, but ditched during production, but in the scene where Wolverine shuts a dam door, saving the X-Men from a wall of water, Jean Grey is the only character not looking at him.

When Jean and Storm are in the church looking for Nightcrawler, Jean is wearing a jacket with a phoenix on the back. This is a nod to the fans of the comic book where Jean becomes Phoenix.

Bruce Davison (Senator Kelly) and Brian Cox (William Stryker) were born only 27 days apart, but Cox's charcter indicates that Senator Kelly is at least 20 years his junior.

Frozen tea was put on the end of Wolverine's claws for the cat at Iceman's home to lick off.

Magneto's line "When will these people learn how to fly?" is a reference to the fact that some of the characters (Jean Grey and Rogue) have the ability to fly in the comics but haven't yet in the films. The only characters with the power of flight in the comics that have shown this ability in the movies are Magneto and Storm.

Ian McKellen (Magneto) worked with screenwriters to make the scene in which Bobby Drake (Ice Man) tells his parents he is a mutant to look more like a common gay "coming-out" scene.